Production and partial characterization of -galactosidase activity from an Antarctic bacterial isolate, Bacillus sp. LX-1

An Antarctic Bacillus sp. isolate was found to exhibit extracellular α-galactosidase activity. On the basis of the results of 16S rRNA sequencing, the strain was named Bacillus sp. LX-1. In a one-factor-at-a-time experiment, galactose, peptone and Mn2+ were found to be the medium components that facilitated enzyme production. The new strain showed optimal α-galactosidase activity at pH 7.0 and temperature of 40°C. The enzyme exclusively hydrolyzed α-D-galactosides such as p-nitrophenyl--galactopyranoside, melibiose, raffinose and stachyose, and showed no effect with proteases such as trypsin, pancreatin, and pronase. Enzyme activity was almost completely inhibited by the presence of Ag+, Hg2+, Cu2+, and sodium dodecylsulfate (SDS) but was unaffected by β-mercaptoethanol and ethylenediaminetetraacetic acid (EDTA). The LX-1 α-galactosidase may be a promising candidate as a biocatalyst for soybean processing in food and feed industries.Key words: Antarctic, Bacillus sp., α-galactosidase, one-factor-at-a-time, biocatalyst

Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection

<p>Abstract</p> <p>Background</p> <p>Nonnegative matrix factorization (NMF) is a feature extraction method that has the property of intuitive part-based representation of the original features. This unique ability makes NMF a potentially promising method for biological sequence analysis. Here, we apply NMF to fold recognition and remote homolog detection problems. Recent studies have shown that combining support vector machines (SVM) with profile-profile alignments improves performance of fold recognition and remote homolog detection remarkably. However, it is not clear which parts of sequences are essential for the performance improvement.</p> <p>Results</p> <p>The performance of fold recognition and remote homolog detection using NMF features is compared to that of the unmodified profile-profile alignment (PPA) features by estimating Receiver Operating Characteristic (ROC) scores. The overall performance is noticeably improved. For fold recognition at the fold level, SVM with NMF features recognize 30% of homolog proteins at > 0.99 ROC scores, while original PPA feature, HHsearch, and PSI-BLAST recognize almost none. For detecting remote homologs that are related at the superfamily level, NMF features also achieve higher performance than the original PPA features. At > 0.90 ROC₅₀scores, 25% of proteins with NMF features correctly detects remotely related proteins, whereas using original PPA features only 1% of proteins detect remote homologs. In addition, we investigate the effect of number of positive training examples and the number of basis vectors on performance improvement. We also analyze the ability of NMF to extract essential features by comparing NMF basis vectors with functionally important sites and structurally conserved regions of proteins. The results show that NMF basis vectors have significant overlap with functional sites from PROSITE and with structurally conserved regions from the multiple structural alignments generated by MUSTANG. The correlation between NMF basis vectors and biologically essential parts of proteins supports our conjecture that NMF basis vectors can explicitly represent important sites of proteins.</p> <p>Conclusion</p> <p>The present work demonstrates that applying NMF to profile-profile alignments can reveal essential features of proteins and that these features significantly improve the performance of fold recognition and remote homolog detection.</p

Quantitative and qualitative investments in internal control personnel and firm operational efficiency: Evidence from Korea

Although internal control systems in firms aim to provide reasonable assurance regarding objectives related to operations, reporting, and compliance, research focusing on operational efficiency is limited. This study investigates the impact of both quantitative and qualitative investments in internal control personnel on a firm’s operational efficiency. Utilizing a fixed-effect regression model, the Heckman (1979) two-stage model, and a two-stage least squares procedure, this study analyzes 4,471 firm-year observations from Korean listed firms from 2018 to 2020. The findings indicate a positive association between investment in internal control personnel and operational efficiency. This relationship remains robust even under sensitivity tests and concerns of potential endogeneity, as confirmed by the Heckman and two-stage least squares models. Specifically, the Heckman model shows that the ratio of the number of employees (coef = 0.023, t-value = 5.20) and certified public accountants (coef = 0.256, t-value = 5.43) responsible for internal control is positively associated with operational efficiency. Average work experience (coef = 0.002, t-value = 1.84) of internal control personnel is also positively related to operational efficiency. This study provides empirical evidence for the significance of investing in internal control personnel to boost operational efficiency and suggests that firms should consider both quantitative and qualitative aspects of internal control

An unconventional platform for two-dimensional Kagome flat bands on semiconductor surfaces

In condensed matter physics, the Kagome lattice and its inherent flat bands have attracted considerable attention for their potential to host a variety of exotic physical phenomena. Despite extensive efforts to fabricate thin films of Kagome materials aimed at modulating the flat bands through electrostatic gating or strain manipulation, progress has been limited. Here, we report the observation of a novel $d$-orbital hybridized Kagome-derived flat band in Ag/Si(111) $\sqrt{3}\times\sqrt{3}$ as revealed by angle-resolved photoemission spectroscopy. Our findings indicate that silver atoms on a silicon substrate form a Kagome-like structure, where a delicate balance in the hopping parameters of the in-plane $d$-orbitals leads to destructive interference, resulting in a flat band. These results not only introduce a new platform for Kagome physics but also illuminate the potential for integrating metal-semiconductor interfaces into Kagome-related research, thereby opening a new avenue for exploring ideal two-dimensional Kagome systems.Comment: 7 pages, 4 figure

Remodeling Pattern of Spinal Canal after Full Endoscopic Uniportal Lumbar Endoscopic Unilateral Laminotomy for Bilateral Decompression: One Year Repetitive MRI and Clinical Follow-Up Evaluation

Objective: There is limited literature on repetitive postoperative MRI and clinical evaluation after Uniportal Lumbar Endoscopic Unilateral Laminotomy for Bilateral Decompression. Methods: Clinical visual analog scale, Oswestry Disability Index, McNab's criteria evaluation and MRI evaluation of the axial cut spinal canal area of the upper end plate, mid disc and lower end plate were performed for patients who underwent single-level Uniportal Lumbar Endoscopic Unilateral Laminotomy for Bilateral Decompression. From the evaluation of the axial cut MRI, four types of patterns of remodeling were identified: type A: continuous expanded spinal canal, type B: restenosis with delayed expansion, type C: progressive expansion and type D: restenosis. Result: A total of 126 patients with single-level Uniportal Lumbar Endoscopic Unilateral Laminotomy for Bilateral Decompression were recruited with a minimum follow-up of 26 months. Thirty-six type A, fifty type B, thirty type C and ten type D patterns of spinal canal remodeling were observed. All four types of patterns of remodeling had statistically significant improvement in VAS at final follow-up compared to the preoperative state with type A (5.59 +/- 1.58), B (5.58 +/- 1.71), C (5.58 +/- 1.71) and D (5.27 +/- 1.68), p &lt; 0.05. ODI was significantly improved at final follow-up with type A (49.19 +/- 10.51), B (50.00 +/- 11.29), C (45.60 +/- 10.58) and D (45.60 +/- 10.58), p &lt; 0.05. A significant MRI axial cut increment of the spinal canal area was found at the upper endplate at postoperative day one and one year with type A (39.16 +/- 22.73; 28.00 +/- 42.57) mm(2), B (47.42 +/- 18.77; 42.38 +/- 19.29) mm(2), C (51.45 +/- 18.16; 49.49 +/- 18.41) mm(2) and D (49.10 +/- 23.05; 38.18 +/- 18.94) mm(2), respectively, p &lt; 0.05. Similar significant increment was found at the mid-disc at postoperative day one, 6 months and one year with type A (55.16 +/- 27.51; 37.23 +/- 25.88; 44.86 +/- 25.73) mm(2), B (72.83 +/- 23.87; 49.79 +/- 21.93; 62.94 +/- 24.43) mm(2), C (66.85 +/- 34.48; 54.92 +/- 30.70; 64.33 +/- 31.82) mm(2) and D (71.65 +/- 16.87; 41.55 +/- 12.92; 49.83 +/- 13.31) mm(2) and the lower endplate at postoperative day one and one year with type A (49.89 +/- 34.50; 41.04 +/- 28.56) mm(2), B (63.63 +/- 23.70; 54.72 +/- 24.29) mm(2), C (58.50 +/- 24.27; 55.32 +/- 22.49) mm(2) and D (81.43 +/- 16.81; 58.40 +/- 18.05) mm(2) at postoperative day one and one year, respectively, p &lt; 0.05. Conclusions: After full endoscopic lumbar decompression, despite achieving sufficient decompression immediately postoperatively, varying severity of asymptomatic restenosis was found in postoperative six months MRI without clinical significance. Further remodeling with a varying degree of increment of the spinal canal area occurs at postoperative one year with overall good clinical outcomes

A randomized, phase II study of gefitinib alone versus nimotuzumab plus gefitinib after platinum-based chemotherapy in advanced non-small cell lung cancer (KCSG LU12-01)

We aimed to evaluate the efficacy of dual inhibition of epidermal growth factor receptor (EGFR) with nimotuzumab (EGFR monoclonal antibody) plus gefitinib (EGFR-tyrosine kinase inhibitor) in advanced non-small cell lung cancer (NSCLC) after platinum-based chemotherapy. An open label, randomized, phase II trial was conducted at 6 centers; 160 patients were randomized (1:1) to either gefitinib alone or nimotuzumab (200 mg, i. v. weekly) plus gefitinib (250 mg p. o. daily) until disease progression or intolerable toxicity. The primary endpoint was progression-free survival (PFS) at 3 months. Of the total 160 enrolled patients, 155 (77: gefitinib, 78: nimotuzumab plus gefitinib) received at least one dose and could be evaluated for efficacy and toxicity. The majority had adenocarcinoma (65.2%) and ECOG performance status of 0 to 1 (83.5%). The median follow-up was 22.1 months, and the PFS rate at 3 months was 48.1% in gefitinib and 37.2% in nimotuzumab plus gefitinib (P = not significant, NS). The median PFS and OS were 2.8 and 13.2 months in gefitinib and 2.0 and 14.0 months in nimotuzumab plus gefitinib. Combined treatment was not associated with superior PFS to gefitinib alone in patients with EGFR mutation (13.5 vs. 10.2 months in gefitinib alone, P=NS) or those with wild-type EGFR (0.9 vs. 2.0 months in gefitinib alone, P=NS). Combined treatment did not increase EGFR inhibition-related adverse events with manageable toxicities. The dual inhibition of EGFR with nimotuzumab plus gefitinib was not associated with better outcomes than gefitinib alone as a second-line treatment of advanced NSCLC (NCT01498562).

Host-mediated beneficial effects of phytochemicals for prevention of avian coccidiosis

Both in vitro and in vivo studies were conducted to evaluate the beneficial effects of green tea extract (GT), cinnamon oil (CO), and pomegranate extract (PO) on avian coccidiosis. In experiment (EXP) 1, an in vitro culture system was used to investigate the individual effects of GT, CO, and PO on the proinflammatory cytokine response and integrity of tight junction (TJ) in chicken intestinal epithelial cells (IEC), on the differentiation of quail muscle cells and primary chicken embryonic muscle cells, and anticoccidial and antibacterial activities against Eimeria tenella sporozoites and Clostridium perfringens bacteria, respectively. In EXP 2 and 3, in vivo trials were carried out to study the dose-dependent effect of blended phytochemicals (GT, CO, PO) on coccidiosis in broiler chickens infected with E. maxima. For EXP 2, one hundred male broiler chickens (0-day-old) were allocated into the following five treatment groups: Control group for non-infected chickens (NC), Basal diet group for E. maxima-infected chickens (PC), PC group supplemented with phytochemicals at 50 (Phy 50), 100 (Phy 100), and 200 (Phy 200) mg/kg feed diets for E. maxima-infected chickens. For EXP 3, one hundred twenty male broiler chickens (0-day-old) were allocated into the following six treatment groups: NC, PC, PC supplemented with phytochemicals at 10 (Phy 10), 20 (Phy 20), 30 (Phy 30), and 100 (Phy 100) mg/kg feed for E. maxima-infected chickens. Body weights (BW) were measured on days 0, 7, 14, 20, and 22, and jejunum samples were used to measure cytokine, TJ protein, and antioxidant enzyme responses at 8 days post-infection (dpi). Fecal samples for oocyst enumeration were collected from 6 to 8 dpi. In vitro, CO and PO reduced LPS-induced IL-1β and IL-8 in IEC, respectively, and GT enhanced the gene expression of occludin in IEC. PO at 1.0 and 5.0 mg/mL exerted antimicrobial effect against E. tenella sporozoites and C. perfringens bacteria, respectively. In vivo, chickens fed a diet supplemented with phytochemicals showed enhanced BW, reduced oocyst shedding, and decreased proinflammatory cytokines following E. maxima challenge. In conclusion, the combination of GT, CO, and PO in the diet of broiler chickens infected with E. maxima induced enhanced host disease resistance including innate immunity and gut health, which contributed to improved growth and reduced disease responses. These findings provide scientific support for the development of a novel phytogenic feed additive formula that enhances the growth and intestinal health of broiler chickens infected with coccidiosis

PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis

Chang Rok Kim, Taichi Noda, Hyunkyung Kim, Gibeom Kim, Seongwan Park, Yongwoo Na, Seiya Oura, Keisuke Shimada, Injin Bang, Jun-Yeong Ahn, Yong Ryoul Kim, Se Kyu Oh, Hee-Jung Choi, Jong-Seo Kim, Inkyung Jung, Ho Lee, Yuki Okada, Masahito Ikawa, Sung Hee Baek, PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis, Cell Reports, Volume 32, Issue 4, 2020, 107950, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2020.107950

The impact of non-pharmaceutical interventions on premature births during the COVID-19 pandemic: a nationwide observational study in Korea

BackgroundNon-pharmaceutical interventions (NPIs), such as social distancing and hand washing, have been associated with a decline in the preterm birth rate worldwide. We aimed to evaluate whether the preterm birth rate in Korea during the coronavirus disease 2019 lockdown has changed compared to that in previous years.MethodA birth registry from the Korea Statistical Information Service, which is a nationwide official database, was used to include all births claimed to have occurred between 2011 and 2020. Newborns with gestational age (GA) less than 22 weeks and birth weight less than 220 g were excluded. The pre-NPI period was designated as January 2011 to January 2020, and the NPI period was defined as February 2020 to December 2020. We assessed the effect of NPI on the incidence of prematurity per 100 births using an interrupted time-series quasi-experimental design and implementing an autoregressive integrated moving average (ARIMA) model.ResultsFrom 2011 to 2020, a total of 3,931,974 live births were registered, among which 11,416 were excluded. Consequently, the final study population included 3,920,558 live births (both singleton and multiple births) among which 275,009 (7.0%) were preterm. The preterm birth rate was significantly higher during the NPI period (8.68%) compared to that in the pre-NPI period (6.92%) (P &lt; 0.001). The ARIMA model showed that in all singleton and multiple births, except those in July (observed 9.24, expected 8.54, [95% prediction interval {PI} 8.13–8.96], percent difference 7.81%), September (observed 7.89, expected 8.35, [95% PI 7.93–8.76], percent difference −5.66%), and December (observed 9.90, expected 9.40, [95% PI 8.98–9.82], percent difference 5.2%), most observed values were within the 95% PI of the expected values and showed an increasing trend.ConclusionIn this nationwide observational study, the trend in premature birth rate did not significantly change due to NPI implementation in Korea, as it had been increasing since 2011. The trend of Korea's birth rate appears to be unaffected by the implementation of NPIs; however, further studies with a longer follow-up period are needed

Immunophenotyping of COVID-19 and influenza highlights the role of type I interferons in development of severe COVID-19

Although most SARS-CoV-2-infected individuals experience mild coronavirus disease 2019 (COVID-19), some patients suffer from severe COVID-19, which is accompanied by acute respiratory distress syndrome and systemic inflammation. To identify factors driving severe progression of COVID-19, we performed single-cell RNA-seq using peripheral blood mononuclear cells (PBMCs) obtained from healthy donors, patients with mild or severe COVID-19, and patients with severe influenza. Patients with COVID-19 exhibited hyper-inflammatory signatures across all types of cells among PBMCs, particularly up-regulation of the TNF/IL-1 beta-driven inflammatory response as compared to severe influenza. In classical monocytes from patients with severe COVID-19, type I IFN response co-existed with the TNF/IL-1 beta-driven inflammation, and this was not seen in patients with milder COVID-19. Interestingly, we documented type I IFN-driven inflammatory features in patients with severe influenza as well. Based on this, we propose that the type I IFN response plays a pivotal role in exacerbating inflammation in severe COVID-19